Run MED
Preparation
Paths and libraries setting
Create fasta file for each Genus
To run oligotyping, we need to create fasta files for each Genus we want analyze.
Wolbachia
Asaia
Chryseobacterium
Elizabethkingia
Erwinia
Legionella
Serratia
Run Oligotyping
Wolbachia
Docker
In a terminal session :
# move in repertory with the fasta file
cd /Volumes/MY_PASSPORT/draft_final/output/oligotyping/wolbachia
# run docker session
sudo docker run --rm -it -v `pwd`:`pwd` -w `pwd` -p 8080:8080 meren/oligotyping:latest
Alignment
# fill gaps
o-pad-with-gaps oligotyping_Wolbachia_sequences.fasta
Shannon entropy
entropy-analysis oligotyping_Wolbachia_sequences.fasta-PADDED-WITH-GAPS
Oligotyping
oligotype oligotyping_Wolbachia_sequences.fasta-PADDED-WITH-GAPS oligotyping_Wolbachia_sequences.fasta-PADDED-WITH-GAPS-ENTROPY -c 2 -M 10
7 oligotypes
Asaia
Docker
In a terminal session :
# move in repertory with the fasta file
cd /Volumes/MY_PASSPORT/draft_final/output/oligotyping/asaia
# run docker session
sudo docker run --rm -it -v `pwd`:`pwd` -w `pwd` -p 8080:8080 meren/oligotyping:latest
Alignment
# fill gaps
o-pad-with-gaps oligotyping_Asaia_sequences.fasta
Shannon entropy
entropy-analysis oligotyping_Asaia_sequences.fasta-PADDED-WITH-GAPS
Oligotyping
oligotype oligotyping_Asaia_sequences.fasta-PADDED-WITH-GAPS oligotyping_Asaia_sequences.fasta-PADDED-WITH-GAPS-ENTROPY -c 5 -M 10
34 oligotypes
Chryseobacterium
Docker
In a terminal session :
# move in repertory with the fasta file
cd /Volumes/MY_PASSPORT/draft_final/output/oligotyping/wolbachia
# run docker session
sudo docker run --rm -it -v `pwd`:`pwd` -w `pwd` -p 8080:8080 meren/oligotyping:latest
Alignment
# fill gaps
o-pad-with-gaps oligotyping_Chryseobacterium_sequences.fasta
Shannon entropy
entropy-analysis oligotyping_Chryseobacterium_sequences.fasta-PADDED-WITH-GAPS
Oligotyping
oligotype oligotyping_Chryseobacterium_sequences.fasta-PADDED-WITH-GAPS oligotyping_Chryseobacterium_sequences.fasta-PADDED-WITH-GAPS-ENTROPY -c 3 -M 10
3 oligotypes
Elizabethkingia
Docker
In a terminal session :
# move in repertory with the fasta file
cd /Volumes/MY_PASSPORT/draft_final/output/oligotyping/wolbachia
# run docker session
sudo docker run --rm -it -v `pwd`:`pwd` -w `pwd` -p 8080:8080 meren/oligotyping:latest
Alignment
# fill gaps
o-pad-with-gaps oligotyping_Elizabethkingia_sequences.fasta
Shannon entropy
entropy-analysis oligotyping_Elizabethkingia_sequences.fasta-PADDED-WITH-GAPS
Oligotyping
oligotype oligotyping_Elizabethkingia_sequences.fasta-PADDED-WITH-GAPS oligotyping_Elizabethkingia_sequences.fasta-PADDED-WITH-GAPS-ENTROPY -c 1 -M 10
2 oligotypes